BioSysBio:abstracts/2007/Guillermo Rodrigo: Difference between revisions

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=Title=
=iGEM 2006 Valencia: EcoliTaster=
'''Author(s): '''<sup>1</sup>G. Rodrigo, <sup>1</sup>J. Carrera & <sup>2</sup>[[User:Jaramillo|A. Jaramillo]]<br>  
'''Author(s): '''G. Rodrigo<sup>1</sup>, P. Tortosa<sup>3</sup>, A.
Aparici<sup>2</sup>, MC. Aroca<sup>2</sup>, J. Carrera<sup>1</sup>, C. Edo<sup>1,2</sup>, G. Fuertes<sup>2</sup>, D. Jiménez<sup>2</sup>, C. Mata<sup>2</sup>, JV. Medrano<sup>2</sup>, A.
Montagud<sup>2</sup>, C. Navarrete<sup>2</sup>, E. Navarro<sup>1</sup>, M. Báguena<sup>1</sup>, P. Fernández de Córdoba<sup>1</sup>, A.
Ferrando<sup>2</sup>, J. Salgado<sup>2</sup>, J. Urchueguía<sup>1</sup>,[[User:Jaramillo|A. Jaramillo]]<sup>3</sup><br>  
'''Affiliations:''' <sup>1</sup>Universidad Politecnica Valencia, Spain  <br>
'''Affiliations:''' <sup>1</sup>Universidad Politecnica Valencia, Spain  <br>
:::<sup>2</sup>Ecole Polytechnique, France <br>
:::<sup>2</sup>Universidad de Valencia, Spain <br>
:::<sup>3</sup>Ecole Polytechnique, France <br>
 
'''Contact:''' http://www.enseignement.polytechnique.fr/profs/biochimie/Alfonso.Jaramillo/
'''Contact:''' http://www.enseignement.polytechnique.fr/profs/biochimie/Alfonso.Jaramillo/
<br>
<br>
'''Keywords:''' 'keyword_1' 'keyword_2'  'keyword_3' 'keyword_4'  
'''Keywords:''' 'iGEM' 'Synthetic Biology'  'Computational Protein Design'


[[Category:BioSysBio Keywords add_keyword_1]]
[[Category:BioSysBio Keywords iGEM]]
[[Category:BioSysBio Keywords add_keyword_2]]
[[Category:BioSysBio Keywords Synthetic Biology]]
[[Category:BioSysBio Keywords add_keyword_3]]
[[Category:BioSysBio Keywords Computational Protein Design]]
[[Category:BioSysBio Keywords add_keyword_4]]






==Background/Introduction==
==Background/Introduction==
Add your text here
<p class=MsoNormal style='text-align:justify;mso-layout-grid-align:none;
text-autospace:none'><span lang=EN-US style='mso-ansi-language:EN-US'>Our
project for this iGEM edition in 2006 [1] is making a cellular biosensor. We
use <i style='mso-bidi-font-style:normal'>E. coli</i> as cellular chassis,
using a deficient <i style='mso-bidi-font-style:normal'>EnvZ</i> strain. We
construct two different modules in order to assemble it: on the one hand,
sensor devices, and on the other, actuators. Firstly, we use membrane proteins
to perform the sensing function, i</span><span lang=EN-US style='mso-ansi-language:
EN-US;mso-fareast-language:ES'>nspired on Hellinga’s work sensing TNT and other
molecules using a mutated periplasmic binding protein (PBP) [2]. Thus, our team
thought in building a PBP that docks a vanillin molecule. It performs an
allosteric motion that makes it binding to the <i>trg </i>protein (Fig. 1).
When the PBP-vanillin complex (Fig. 2) binds <i>trg</i>, then an allosteric
motion is propagated to the EnvZ kinase domain resulting in autophosphorylation
and phosphate transfer to OmpR transcription factor (OmpR-P). Secondly, </span><span
lang=EN-US style='mso-ansi-language:EN-US'>we use a genetic synthetic network
as actuator that at high input levels has a given fluorescent response and at
low levels other (Fig. 3). Therefore, for intermediate levels there is a
gradient if we superpose the colors. To get that behavior, we construct two
branches with different strengths, and we use a synthetic promoter activated by
two transcription factors: cI and CRP [3]. In addition, this promoter can be
understood as an AND logic gate (see promoter behavior in Fig. 4, and see its
construction in Fig. 5).<o:p></o:p></span></p>


==Results==
==Results==
Line 30: Line 56:


==References==
==References==
[1]
http://parts.mit.edu/wiki/index.php/UPV-UV_Valencia%2C_Spain_2006
[2] L.L. Looger,
M.A. Dwyer, J. Smith, and H.W. Hellinga. Computational design of receptor and sensor
proteins with novel functions. <i>Nature</i>,
423, 185-190 (2003).
[3] J.K. Joung,
D.M. Koepp, and A. Hochschild. Synergistic activation of transcription by
bacteriophage lambda cI protein and E. coli cAMP receptor protein. <i>Science</i>,
265, 1863-1866 (1994).


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Revision as of 08:06, 29 September 2006

iGEM 2006 Valencia: EcoliTaster

Author(s): G. Rodrigo1, P. Tortosa3, A. Aparici2, MC. Aroca2, J. Carrera1, C. Edo1,2, G. Fuertes2, D. Jiménez2, C. Mata2, JV. Medrano2, A. Montagud2, C. Navarrete2, E. Navarro1, M. Báguena1, P. Fernández de Córdoba1, A. Ferrando2, J. Salgado2, J. Urchueguía1,A. Jaramillo3
Affiliations: 1Universidad Politecnica Valencia, Spain

2Universidad de Valencia, Spain
3Ecole Polytechnique, France

Contact: http://www.enseignement.polytechnique.fr/profs/biochimie/Alfonso.Jaramillo/
Keywords: 'iGEM' 'Synthetic Biology' 'Computational Protein Design'


Background/Introduction

Our project for this iGEM edition in 2006 [1] is making a cellular biosensor. We use E. coli as cellular chassis, using a deficient EnvZ strain. We construct two different modules in order to assemble it: on the one hand, sensor devices, and on the other, actuators. Firstly, we use membrane proteins to perform the sensing function, inspired on Hellinga’s work sensing TNT and other molecules using a mutated periplasmic binding protein (PBP) [2]. Thus, our team thought in building a PBP that docks a vanillin molecule. It performs an allosteric motion that makes it binding to the trg protein (Fig. 1). When the PBP-vanillin complex (Fig. 2) binds trg, then an allosteric motion is propagated to the EnvZ kinase domain resulting in autophosphorylation and phosphate transfer to OmpR transcription factor (OmpR-P). Secondly, we use a genetic synthetic network as actuator that at high input levels has a given fluorescent response and at low levels other (Fig. 3). Therefore, for intermediate levels there is a gradient if we superpose the colors. To get that behavior, we construct two branches with different strengths, and we use a synthetic promoter activated by two transcription factors: cI and CRP [3]. In addition, this promoter can be understood as an AND logic gate (see promoter behavior in Fig. 4, and see its construction in Fig. 5).<o:p></o:p>

Results

Add your text here

Images/Tables

Add your images or tables here

Materials/Methods

Add your text here

Conclusion

Add your text here

References

[1] http://parts.mit.edu/wiki/index.php/UPV-UV_Valencia%2C_Spain_2006

[2] L.L. Looger, M.A. Dwyer, J. Smith, and H.W. Hellinga. Computational design of receptor and sensor proteins with novel functions. Nature, 423, 185-190 (2003).

[3] J.K. Joung, D.M. Koepp, and A. Hochschild. Synergistic activation of transcription by bacteriophage lambda cI protein and E. coli cAMP receptor protein. Science, 265, 1863-1866 (1994).


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